[eschaider]

You are experiencing an engine controls problem, possibly sensor-based, wiring harness-based, ECU based, or perhaps tune-based. The shortest solution to the problem resolution would be to data log the engine's primary systems, i.e. fueling, air, and spark. The answer will be in one or more of those systems, and the data logging will show which is getting crazy and under what conditions it is occurring so you know what to go after.

You did not say which EFI system you are using. If it is one of Ford's, then you will need to use whatever they offer for data logging. If it is an aftermarket system, then you will have a data logging capability that was part of the EFI engine control system package to solve the puzzle.

Until you start to data log engine operations to determine what is or is not happening, when these events occur, you are making wild-ass guesses at the problem that are not even scientific wild-ass guesses. The technology exists to quickly determine what is going wrong and take appropriate corrective action. All you have to do is find it and of course, know how to use it.

If your ECU is one of the Ford offerings through FRPP, contact them directly and ask about their diagnostic software tools availability. In a best-case scenario, a Ford dealership should be able to use its dealership diagnostic tools to determine what is going wrong. That, of course, assumes you have one nearby who is interested in helping. The challenge you will have with the dealership solution set is the car is not an OEM production vehicle, and even though it uses a Ford engine management system, they will be reluctant to become engaged in what they may well view as a problem-solving adventure.

Once outside the US, the number of performance-related firms and diagnostic services for custom applications, like yours, diminishes but does not disappear. They can be more expensive once you do find them compared to a similar service provider Stateside.

If all attempts at problem resolution fail, there is always the replace the EFI system solution set with a known capable aftermarket alternative. If that is the path you get forced down, the choice of replacement EFI system is only a part of the complete solution set. After the replacement system has been identified, you will need a service provider to install it and a knowledgeable, experienced dyno shop to tune it.

If you are knowledgeable about EFI systems, you might be able to do the installation yourself. The questions in your post tend to belie that sort of familiarity.